Hi, Robert:
Can you explain more detail about "Jmol can communicate over ports to other
programs." ?
Can I do that in Jmol application command line system or in Jmol applet?
Thank you.
On Sat, Sep 14, 2013 at 5:48 PM,
<[email protected]>wrote:
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> Today's Topics:
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> 1. Re: corrupt download? (Robert Hanson)
> 2. Re: Jmol-users Digest, Vol 88, Issue 22 Message: 2 Re: Link
> Jmol to other programme (Robert Hanson)
> 3. Re: JSmol loading local files from remote page (Amjad Farooq)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 14 Sep 2013 13:45:22 -0500
> From: Robert Hanson <[email protected]>
> Subject: Re: [Jmol-users] corrupt download?
> To: "[email protected]"
> <[email protected]>
> Message-ID:
> <CAF_YUvWzO=
> [email protected]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> OK, I will look into that. It was a very slow hotel upload. As soon as I
> get
>
> WRITE FILE
>
> working, I'll get that uploaded. This is also available at
>
> http://chemapps.stolaf.edu/jmol/zip/Jmol.zip
>
> Bob
>
>
>
> On Fri, Sep 13, 2013 at 3:40 PM, Greg Edwards <[email protected]> wrote:
>
> > Me too. I have been working with 13.0.18 as a stopgap.
> >
> >
> > On 14 September 2013 06:13, Vinushka Schalk <[email protected]
> >wrote:
> >
> >> I can report the same issue. I've been having trouble downloading it as
> >> well.
> >>
> >>
> >> On Fri, Sep 13, 2013 at 11:39 AM, Angel Herr?ez <[email protected]
> >wrote:
> >>
> >>> I'm downloading JSmol:
> >>>
> >>> http://sourceforge.net/projects/jsmol/files/
> >>>
> >>> 13.2.4 is 43 MB
> >>> 13.3.4 is 43 MB
> >>> 13.3.5 is only 34 MB and does not open in WinZip (corrupt file)
> >>>
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------------
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> >>>
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> How ServiceNow helps IT people transform IT departments:
> >> 1. Consolidate legacy IT systems to a single system of record for IT
> >> 2. Standardize and globalize service processes across IT
> >> 3. Implement zero-touch automation to replace manual, redundant tasks
> >>
> >>
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> >>
> >>
> >
> >
> > --
> > Greg Edwards,
> > Port Jackson Bioinformatics
> > [email protected]
> >
> >
> >
> ------------------------------------------------------------------------------
> > How ServiceNow helps IT people transform IT departments:
> > 1. Consolidate legacy IT systems to a single system of record for IT
> > 2. Standardize and globalize service processes across IT
> > 3. Implement zero-touch automation to replace manual, redundant tasks
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk
> > _______________________________________________
> > Jmol-users mailing list
> > [email protected]
> > https://lists.sourceforge.net/lists/listinfo/jmol-users
> >
> >
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 2
> Date: Sat, 14 Sep 2013 13:51:07 -0500
> From: Robert Hanson <[email protected]>
> Subject: Re: [Jmol-users] Jmol-users Digest, Vol 88, Issue 22 Message:
> 2 Re: Link Jmol to other programme
> To: "[email protected]"
> <[email protected]>
> Message-ID:
> <
> caf_yuvvrafcmc8ow5i-qefa33xdk_cyb5aesobmxmxpfsuq...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> What are your means of "calling another program?"
>
> If you mean a command-line system call, Jmol is not set up for that. THAT
> would be a serious security issue. Not going to happen. But Jmol can
> communicate over ports to other programs, and so you could do that.
>
> What goes on between (1) and (2)? Presumably something, or there would be
> no need for Jmol. What is the "other program"? Can it be called via
> http://localhost ? That would be another way to communicate.
>
> Bob
>
>
>
> On Fri, Sep 13, 2013 at 11:26 AM, jiayi.zhou <[email protected]> wrote:
>
> > Message 2
> > Re: [Jmol-users] Link Jmol to other programme
> >
> > Hi, Robert:
> >
> > Did you mean I cannot link Jmol to other program just by using script in
> a
> > running Jmol application. I have to embed Jmol to other program?
> >
> > I am trying to do the following things using Jmol script.
> > 1. read in 2 structure files
> > 2. call an external program to change the atom order of one structure
> file
> > and pass back the new structure file to Jmol
> > 3. Display the 2 structures.
> >
> > I'd like to know when I use "load" to read in the files in Jmol. How can
> I
> > get the information of the structure file? Will Jmol create an object of
> it
> > and I can use this object to get all the atom information such as
> > coordinates and connectivity matrix,etc?
> > If I can do that, I plan to use "message" command to pass these
> > information to external program and pass back the result by a call-back
> > function.
> > Then I can use Jmol to display the structures.
> >
> > Thank you.
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 3
> Date: Sat, 14 Sep 2013 16:18:40 -0400
> From: Amjad Farooq <[email protected]>
> Subject: Re: [Jmol-users] JSmol loading local files from remote page
> To: [email protected]
> Message-ID:
> <
> cae1yu5gb2f81ydsyhfv-df7hepjbvb91dxb8svmxbtnac4j...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Bob,
>
> Thanks for the new JSmol copy. I just tested it on Firefox 23 and it seems
> faster than the previous version.
>
> Also, the following commands are working on my side too:
> "load ?.pdb"
> "write JPG ?.jpg "
> "write PNG ?.png "
>
> but these commands do not work yet:
> "write FILE ?.pdb "
> or
> "write PDB ?.pdb "
>
> Please let me know when you have time to test these as well.
>
> Thank you very much!
> Amjad
>
>
>
>
>
> On Sat, Sep 14, 2013 at 2:43 PM, Robert Hanson <[email protected]> wrote:
>
> > way ahead of you.
> >
> >
> > On Fri, Sep 13, 2013 at 3:50 PM, Amjad Farooq <[email protected]>
> wrote:
> >
> >>
> >> (1) Please also enable file save feature (in other words, allow users to
> >> save PDB coordinates from JSmol onto their local machine).
> >>
> >>
> > WRITE FILE "xxx.pdb"
> >
> > But I see that's not quite working right yet.
> >
> >
> >
> >
> >> (2) The image save (PNG) is working fine but it may be good to also add
> >> JPG and TIFF options as some people prefer these formats.
> >>
> >>
> > WRITE JPG 600 600 "xxx.jpg"
> >
> > is working, at least in Firefox, Chrome, and MSIE -- what I have to test
> > here.
> >
> >
> > TIFF is not available. Plenty of converters out there.
> >
> >
> >
> >> (3) Once the above features are available, can you please make the new
> >> version of JSmol available to us. I am gonna switch to JSmol
> altogether. No
> >> a big fan of Java.
> >>
> >>
> > it's in
> >
> > http://chemapps.stolaf.edu/jmol/zip/Jmol.zip
> >
> >
> > Bob
> >
> >
> > --
> > Robert M. Hanson
> > Larson-Anderson Professor of Chemistry
> > St. Olaf College
> > Northfield, MN
> > http://www.stolaf.edu/people/hansonr
> >
> >
> > If nature does not answer first what we want,
> > it is better to take what answer we get.
> >
> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
> >
> >
> >
> >
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> >
> >
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>
> End of Jmol-users Digest, Vol 88, Issue 36
> ******************************************
>
--
Aiden/Jiayi Zhou
Office Tel: 709-864-4891
Master Candidate
Dept. of Computer Science
Memorial University of Newfoundland
St. John's, NL, Canada, A1B 3X5
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